R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 12 found.
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PolyPeakParser (Package: sangerseqR) : Run Poly Peak Parser

Runs the Poly Peak Parser shiny (shiny.rstudio.com) app in the system's default browser. Poly Peak Parser is a web front end that reads, plots and parses double peaks from chromatogram files. Instructions can be found on the webpage once it launches.

● Data Source: BioConductor
● Keywords:
● Alias: PolyPeakParser
● 0 images

abif-class (Package: sangerseqR) : ABIF Class Objects

S4 object returned by read.abif containing all fields in the ABIF file format (see http://home.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf). Data fields vary by machine and basecaller versions. Must be converted to sangerseq to be used in other functions from this package.

● Data Source: BioConductor
● Keywords:
● Alias: abif, abif-class
● 0 images

chromatogram (Package: sangerseqR) : Generate Chromatogram

Generates a chromatogram from a sangerseq class object.

● Data Source: BioConductor
● Keywords:
● Alias: chromatogram, chromatogram,sangerseq-method
● 0 images

makeBaseCalls (Package: sangerseqR) : Make Basecalls

Updates a sangerseq class object to contain primary and secondary peak calls.

● Data Source: BioConductor
● Keywords:
● Alias: makeBaseCalls, makeBaseCalls,sangerseq-method
● 0 images

read.abif (Package: sangerseqR) : Read ABIF Files

Reads ABIF sanger sequencing data files. ABIF files are a proprietary binary sanger sequencing chromatogram data file created by Applied Biosystems (see http://home.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf). The file is read and parsed into an abif class object. This method is based on the read.abif function in the seqinr package available on CRAN.

● Data Source: BioConductor
● Keywords:
● Alias: read.abif
● 0 images

read.scf (Package: sangerseqR) : Read Scf Files

Reads Scf sanger sequencing data files. Scf files are an open source binary sanger sequencing chromatogram data file (see http://staden.sourceforge.net/manual/formats_unix_2.html). The file is read and parsed into an scf class object.

● Data Source: BioConductor
● Keywords:
● Alias: read.scf
● 0 images

readsangerseq (Package: sangerseqR) : Read Scf or ABIF Files

This is a convienience function for reading Scf or ABIF files into a sangerseq object, which can be used by the other sangerseq package functions. It is equivalent to calling read.scf or read.abif as appropriate and then calling sangerseq.

● Data Source: BioConductor
● Keywords:
● Alias: readsangerseq
● 0 images

sangerseq-class (Package: sangerseqR) : Sangerseq Class Objects

Sangerseq Class Objects contain data necessary for using sangerseq package functions (e.g. chromatogram, makeBaseCalls). The exact content will depend on the source of the data (for example, scf files do not have secondary Basecalls).

● Data Source: BioConductor
● Keywords:
● Alias: sangerseq, sangerseq,abif-method, sangerseq,scf-method, sangerseq-class
● 0 images

primarySeqID (Package: sangerseqR) : Sangerseq Accessor Functions

Accessor Functions allow the user to retrieve results from and assign values to sangerseq-class objects.

● Data Source: BioConductor
● Keywords:
● Alias: peakAmpMatrix, peakAmpMatrix,sangerseq-method, peakAmpMatrix<-, peakAmpMatrix<-,sangerseq-method, peakPosMatrix, peakPosMatrix,sangerseq-method, peakPosMatrix<-, peakPosMatrix<-,sangerseq-method, primarySeq, primarySeq,sangerseq-method, primarySeq<-, primarySeq<-,sangerseq-method, primarySeqID, primarySeqID,sangerseq-method, primarySeqID<-, primarySeqID<-,sangerseq-method, secondarySeq, secondarySeq,sangerseq-method, secondarySeq<-, secondarySeq<-,sangerseq-method, secondarySeqID, secondarySeqID,sangerseq-method, secondarySeqID<-, secondarySeqID<-,sangerseq-method, traceMatrix, traceMatrix,sangerseq-method, traceMatrix<-, traceMatrix<-,sangerseq-method
● 0 images

sangerseqR-package (Package: sangerseqR) :

This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms.

● Data Source: BioConductor
● Keywords:
● Alias: sangerseqR, sangerseqR-package
● 0 images